tbuckley/cabot-search huggingface dataset:
Abstract A022: A field survey of histone PTM antibodies in epigenomic mapping approaches reveals widespread liabilities: Best practices and resources for reliable epigenetic studies
Authors: Andrea L. Johnstone, Danielle N. Maryanski, Keli L. Rodriguez, Ellen N. Weinzapfel, Bryan J. Venters, Katherine Novitzky, Matthew R. Marunde, Carolina P. Lin, Michael-Christopher Keogh
Journal: Cancer Research (2022)

Abstract Histone post-translational modifications (PTMs) play a critical role in chromatin regulation. It has long been suspected that the poorly understood capability of ‘PTM-specific’ antibodies (i.e., their specificity and efficiency) is a prime driver of the reproducibility crisis in biomedical research. Here we confirm the validity of this concern as it applies to epigenomic mapping studies. Extensive spike-in panels of PTM-defined DNA-barcoded nucleosome standards show that &amp;gt;70% of &amp;gt;500 commercial antibodies (and &amp;gt;80% of the most highly cited) to &amp;gt;50 histone lysine methyl and acyl states have failing performance in ChIP (&amp;gt;20% cross reactivity/&amp;lt;5% target recovery; www.ChromatinAntibodies.com). Variable lot behavior (of both polyclonals and monoclonals) shows the danger of focusing on catalog numbers without considering the inherent variability of biological reagents. Ultimately, these studies support the inclusion of in situ standards to control genomic mapping assays as an improved path out of this morass. Despite these advances, the application of ChIP-seq for cancer research has been hampered by its requirement for high cell inputs and low reliability. The recent development of immunotethering assays, such as Cleavage Under Targets and Release Using Nuclease (CUT&amp;RUN), deliver high signal-to-noise mapping data using a fraction of the required cells compared to ChIP-seq. These innovations enable the application of epigenomics for cancer research, particularly for primary cells, sorted populations, and clinical samples where cell numbers are limited. By adapting our nucleosome spike-in control approach for CUT&amp;RUN assays, we show that while the same antibody problems observed in ChIP-seq also pervade CUT&amp;RUN, continuous use of spike-in controls improves assay rigor and reproducibility to realize the potential of CUT&amp;RUN to advance cancer research. Citation Format: Andrea L. Johnstone, Danielle N. Maryanski, Keli L. Rodriguez, Ellen N. Weinzapfel, Bryan J. Venters, Katherine Novitzky, Matthew R. Marunde, Carolina P. Lin, Michael-Christopher Keogh. A field survey of histone PTM antibodies in epigenomic mapping approaches reveals widespread liabilities: Best practices and resources for reliable epigenetic studies. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Epigenomics; 2022 Oct 6-8; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_2):Abstract nr A022.
Abstract B006: PBRM1-deficient PBAF complexes target de novo genomic loci to activate NF-κB pathway in kidney cancer
Authors: Xiaosai Yao, Jing Han Hong, Amrita Nargund, Bin Tean Teh
Journal: Cancer Research (2022)

Abstract Polybromo-1 (PBRM1) is the second most commonly mutated gene in kidney cancer after VHL, occurring at a frequency of 30-40%. PBRM1 loss represents a tumor-initiating event and the combined loss of VHL and PBRM1 is necessary and sufficient for renal malignancy. Functionally, PBRM1 is the defining subunit of the polybromo BRG1-associated factor (PBAF) subclass of SWItch/Sucrose Non-Fermentable (SWI/SNF) remodeling complex which regulates chromatin accessibility by sliding, depositing or evicting nucleosomes. Determining context-specific chromatin remodeling by PBRM1 is paramount to understanding how PBRM1 deficiency drives kidney tumorigenesis. We compared the association of SWI/SNF subunits in the presence or absence of PBRM1 and found that PBRM1 loss resulted in a PBAF complex that has undergone alterations in its configuration and targeting specificity: First, the histone binding lobe disengages from the central ATPase subunit. Second, the PBRM1-deficient complexes, despite retaining the DNA binding lobe, occupy aberrant sites, redistributing from promoter proxy regions to distal enhancer regions. The aberrant sites mapped to regions enriched for NF-κB motifs. Indeed, PBRM1-deficient tumors show enhanced NF-κB activity across isogenic tumor models, genetically modified mouse models and clinical samples. We believe that the PBRM1-deficient PBAF complexes enhance the recruitment of nuclear factor RELA, a subunit of the NF-κB complex - this recruitment requires the ATPase function of the SWI/SNF complexes since BRG1/BRM ATPase inhibitor dampens the expression of NF-κB target genes and RELA chromatin occupancy. Proteasome inhibitor bortezomib reverses NF-κB activity by reducing RELA binding at regions bound by PBRM1-deficient PBAF and delays PBRM1-deficient tumor growth. In conclusion, the PBRM1 tumor suppressor safeguards the chromatin by repressing aberrant liberation of pro-tumorigenic NF-κB target genes by residual PBRM1-deficient PBAF complexes. Inhibition of NF-κB activity by bortezomib could be a therapeutic strategy for PBRM1-deficient kidney cancer. Citation Format: Xiaosai Yao, Jing Han Hong, Amrita Nargund, Bin Tean Teh. PBRM1-deficient PBAF complexes target de novo genomic loci to activate NF-κB pathway in kidney cancer. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Epigenomics; 2022 Oct 6-8; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_2):Abstract nr B006.
Abstract A032: MUC1-C regulates chromatin remodeling and drives the CSC state in human cancers
Authors: trayee Bhattacharya, Atsushi Fushimi, Nami Yamashita, Tao Liu, Song Liu, Donald W. Kufe
Journal: Cancer Research (2022)

Abstract The oncogenic MUC1-C protein evolved in mammals to protect epithelial barrier tissues from the external environment. Chronic activation of MUC1-C promotes lineage plasticity, epigenetic reprogramming, and carcinogenesis. MUC1-C also induces the Yamanaka Pluripotency factors. Chromatin remodeling is critical for the cancer stem cell (CSC) state. Our studies have demonstrated that MUC1-C regulates chromatin remodeling by (i) activating the EZH2/PRC2 complex leading to H3K27 trimethylation, and (ii) the BMI1/PRC1 complex with H2A ubiquitylation. In addition, MUC1-C regulates global changes in chromatin accessibility that are mediated at least in part by JUN/AP-1 and ARID1A/BAF in association with driving the CSC state. We also found that silencing MUC1-C suppresses bulk H3K4 trimethylation and H3K27 acetylation levels in diverse human cancer cells. The COMPASS family of H3K4 methyl transferases (HMT) methylate histone H3K4 and the histone acetyl transferase (HAT) p300/CBP family catalyzes H3K27 acetylation. Involvement of MUC1-C in the regulation of COMPASS has not been previously reported. This study demonstrates that MUC1-C induces COMPASS SET1A and WDR5 gene expression by NF-kB p65-mediated transactivation. WDR5 is required for SET1A complex HMT activity. We found that MUC1-C and WDR5 are necessary for expression of FOS, ATF3 and other AP-1 family members. In a positive feedback loop, MUC1-C, WDR5 and AP-1 were shown to be responsible for induction of genes encoding effectors, including TRAF1 and RELB, in the chronic NF-kB inflammatory response. We also found that MUC1-C, NF-kB, WDR5 and AP-1 are necessary for induction of the (i) KLF4 master regulator of the pluripotency network, and (ii) NOTCH1 effector of stemness. Mechanistically, MUC1-C/NF-kB complexes recruit SET1A/WDR5 and AP-1 to enhancer-like signatures in these target genes, increase the deposition of H3K4me3 with the opening of chromatin, and activate their transcription. These findings demonstrate that MUC1-C activates the COMPASS SET1A/WDR5 complex in integrating the induction of genes that promote chronic inflammation, pluripotency, and the CSC state. Citation Format: trayee Bhattacharya, Atsushi Fushimi, Nami Yamashita, Tao Liu, Song Liu, Donald W. Kufe. MUC1-C regulates chromatin remodeling and drives the CSC state in human cancers. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Epigenomics; 2022 Oct 6-8; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_2):Abstract nr A032.
Abstract PR006: Single-molecule and single-cell epigenetics: Decoding the epigenome for cancer research and diagnostics
Authors: Efrat Shema
Journal: Cancer Research (2022)

Abstract Genes and genomic elements are packaged by chromatin structures that regulate their activity. We developed a novel high-throughput single-molecule imaging technology to decode combinatorial modifications on millions of individual nucleosomes. We apply this technology to image nucleosomes and delineate their combinatorial epigenetic patterns, and how these patterns are deregulated in cancer. In addition, we adapt single-cell technologies based on CyTOF to profile the global levels of multiple histone modifications in single cells, thus revealing epigenetic heterogeneity in cancer. Our research focuses on pediatric gliomas harboring lysine to methionine substitution of residue 27 on histone H3 (K27M). We provide evidence for widespread effects of the H3-K27M oncohistone on multiple core epigenetic pathways, and highlight the capability of single-molecule and single-cell tools to reveal mechanisms of chromatin deregulation and heterogeneity in cancer. We also harness the single-molecule technology as a novel liquid biopsy approach, by comprehensively profiling combinatorial epigenetic marks of plasma-isolated nucleosomes. Applying this analysis to a cohort of plasma samples detect colorectal cancer at high accuracy and sensitivity, even at early stages. Finally, combining this proteomic analysis with single-molecule DNA sequencing reveals the tissue-of-origin of the tumor. Citation Format: Efrat Shema. Single-molecule and single-cell epigenetics: Decoding the epigenome for cancer research and diagnostics. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Epigenomics; 2022 Oct 6-8; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_2):Abstract nr PR006.
Abstract IA004: Novel inhibitors of histone H2B deubiquitinating enzymes
Authors: Cynthia Wolberger
Journal: Cancer Research (2022)

Abstract Histone H2B-K120 is dynamically ubiquitinated and deubiquitinated during transcription and is a hallmark of actively transcribed genes. The Spt-Ada-Gcn5 acetyltransferase (SAGA) transcriptional coactivator contains a four-protein subcomplex called the deubiquitinating enzyme (DUB) module that removes ubiquitin from histone H2B-K120. The human DUB module contains the catalytic subunit ubiquitin-specific protease 22 (USP22), which is overexpressed in a number of cancers that are resistant to available therapies. We screened a massive combinatorial library of cyclic peptides and identified potent inhibitors of USP22. The top hit was highly specific for USP22 compared with a panel of 44 other human DUBs. Cells treated with peptide had increased levels of H2B monoubiquitination, demonstrating the ability of the cyclic peptides to enter human cells and inhibit H2B deubiquitination. These macrocycle inhibitors are, to our knowledge, the first reported inhibitors of USP22/SAGA DUB module and show promise for drug development. Citation Format: Cynthia Wolberger. Novel inhibitors of histone H2B deubiquitinating enzymes. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Epigenomics; 2022 Oct 6-8; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_2):Abstract nr IA004.
Abstract B004: Analysis of epigenetic marks and mechanisms in disease: Your guide to a successful assay
Authors: Christopher C. Comeau, Angela H. Guo, Fang Chen, Christopher J. Fry
Journal: Cancer Research (2022)

Abstract Like the chromatin immunoprecipitation (ChIP) assay, Cleavage Under Targets &amp; Release Using Nuclease is a powerful and versatile technique used for probing protein-DNA interactions within the natural chromatin context of the cell. The assay can be combined with downstream qPCR or NG-seq to analyze histone modifications and binding of transcription factors, DNA replication factors, or DNA repair proteins at specific target genes or across the entire genome. It provides a rapid, robust, and true low cell number assay for detection of protein-DNA interactions in the cell. Unlike the ChIP assay, it is free from formaldehyde cross-linking, chromatin fragmentation, and immunoprecipitation. Previously, we have shown that, compared to ChIP, it requires fewer starting cells (100K), has a much faster protocol (one day from cells to DNA), generates lower background signal (requires less sequencing depth), and offers spike-in control DNA for effective normalization of signal between samples and between experiments. We recently updated the CST Assay Kit for use with 5,000-20,000 cells and added protocols for fixed cells and tissue. I will discuss the basics of the assay and important factors to consider when setting up your experiment. In addition, I will provide data showing the versatility of this assay for mapping various histone modifications, transcription factor, and transcription cofactor binding across multiple sample types. Finally, I will discuss how the general protocol is optimized for greater signal to noise ratio, reduced number of starting cells, and provide an alternative digestion method to prepare the input DNA as a critical control of the experiment. Citation Format: Christopher C. Comeau, Angela H. Guo, Fang Chen, Christopher J. Fry. Analysis of epigenetic marks and mechanisms in disease: Your guide to a successful assay. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Epigenomics; 2022 Oct 6-8; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_2):Abstract nr B004.
Abstract A026: Epigenetic factor competition reshapes the EMT landscape
Authors: M. Ali Al-Radhawi, Shubham Tripath, Yun Zhang, Eduardo Sontag, Herbert Levine
Journal: Cancer Research (2022)

Abstract The emergence of and transitions between distinct phenotypes in isogenic cells can be attributed to the intricate interplay of epigenetic marks, external signals, and gene regulatory elements. These elements include chromatin remodelers, histone modifiers, transcription factors, and regulatory RNAs. Mathematical models known as Gene Regulatory Networks (GRNs) are an increasingly important tool to unravel the workings of such complex networks. In such models, epigenetic factors are usually proposed to act on the chromatin regions directly involved in the expression of relevant genes. However, it has been well-established that these factors operate globally and compete with each other for targets genome-wide. Therefore, a perturbation of the activity of a regulator can redistribute epigenetic marks across the genome and modulate the levels of competing regulators. These interactions have been brought to the fore by recent experiments (Zhang, Donaher et al, 2022) reporting that the knockouts of different histone methyltransferases can induce two distinct trajectories of EMT, characterized by distinct and unexpected changes in gene expression profiles. In this work, we propose a new modeling framework that combines local transcriptional regulation with global epigenetic control, and show that complex interplay between transcriptional and epigenetic control can lead to rich gene expression dynamics. We use our modeling framework to understand the effects of various epigenetic perturbations on the epithelial-mesenchymal transition, a crucial cellular process involved in both health and disease. We note that the interplay between epigenetic competition, the EMT transcriptional network, and the baseline transcriptional context can result in counter-intuitive experimental observations, and generate unique paths for cells to transition between epithelial and mesenchymal states. We apply our modeling framework to explain the aforementioned recent experimental findings (Zhang, Donaher et al, 2022), and we use it to offer verifiable predictions. One crucial takeaway from our modeling is that experiments involving epigenetic perturbations must be analyzed with care due to the possibility of widespread cross-talk between the genomic targets of different epigenetic factors. This means that the biological consequence of perturbation to an epigenetic modifier could be an outcome of changes in the expression levels of its direct genomic targets or simply a side-effect from the dilution and distribution of an entirely different epigenetic modifier. Citation Format: M. Ali Al-Radhawi, Shubham Tripath, Yun Zhang, Eduardo Sontag, Herbert Levine. Epigenetic factor competition reshapes the EMT landscape. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Epigenomics; 2022 Oct 6-8; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_2):Abstract nr A026.
Effect of orthopedic and functional orthodontic treatment in children with obstructive sleep apnea: A systematic review and meta-analysis
Authors: Rosaria Bucci, Roberto Rongo, Benedetta Zunino, Ambrosina Michelotti, Paolo Bucci, Giulio Alessandri-Bonetti, Serena Incerti-Parenti, Vincenzo D’Antò
Journal: Sleep Medicine Reviews (2022)

Orthodontic treatment is suggested in growing individuals to correct transverse maxillary deficiency and mandibular retrusion. Since, as a secondary effect, these orthodontic procedures may improve pediatric obstructive sleep apnea (OSA), this systematic review assessed their effects on apnea-hypopnea index (AHI) and oxygen saturation (SaO2). Twenty-five (25) manuscripts were included for qualitative synthesis, 19 were selected for quantitative synthesis. Five interventions were analyzed: rapid maxillary expansion (RME, 15 studies), mandibular advancement (MAA, five studies), myofunctional therapy (MT, four studies), and RME combined with MAA (one study). RME produced a significant AHI reduction and minimum SaO2 increase immediately after active treatment, at six and 12 months from baseline. A significant AHI reduction was also observed six and 12 months after the beginning of MAA treatment. MT showed positive effects, with different protocols. In this systematic review and meta-analysis of data from mainly uncontrolled studies, interceptive orthodontic treatments showed overall favorable effects on respiratory outcomes in pediatric OSA. However, due to the low to very low level of the body evidence, this treatment cannot be suggested as elective for OSA treatment. An orthodontic indication is needed to support this therapy and a careful monitoring is required to ensure positive improvement in OSA parameters.
Viral dynamics of omicron BA.2.76 variant of SARS-CoV-2 in a cohort of COVID-19 patients
Authors: Kangguo Li, Demeng Wang, Huimin Qu, Jia Rui, Buasiyamu Abudunaibi, Zhinan Guo, Sihan Wu, Guzainuer Abudurusuli, Zimei Yang, Kang Fang, Yidun Zhang, Chenghao Su, Tianmu Chen
Journal: Journal of Infection (2022)
METTL4-mediated nuclear N6-deoxyadenosine methylation promotes metastasis through activating multiple metastasis-inducing targets
Authors: Kai-Wen Hsu, Joseph Chieh-Yu Lai, Jeng-Shou Chang, Pei-Hua Peng, Ching-Hui Huang, Der-Yen Lee, Yu-Cheng Tsai, Chi-Jung Chung, Han Chang, Chao-Hsiang Chang, Ji-Lin Chen, See-Tong Pang, Ziyang Hao, Xiao-Long Cui, Chuan He, Kou-Juey Wu
Journal: Genome biology (2022)

Abstract Background DNA N6-methyldeoxyadenosine (6mA) is rarely present in mammalian cells and its nuclear role remains elusive. Results Here we show that hypoxia induces nuclear 6mA modification through a DNA methyltransferase, METTL4, in hypoxia-induced epithelial-mesenchymal transition (EMT) and tumor metastasis. Co-expression of METTL4 and 6mA represents a prognosis marker for upper tract urothelial cancer patients. By RNA sequencing and 6mA chromatin immunoprecipitation-exonuclease digestion followed by sequencing, we identify lncRNA RP11-390F4.3 and one novel HIF-1α co-activator, ZMIZ1, that are co-regulated by hypoxia and METTL4. Other genes involved in hypoxia-mediated phenotypes are also regulated by 6mA modification. Quantitative chromatin isolation by RNA purification assay shows the occupancy of lncRNA RP11-390F4.3 on the promoters of multiple EMT regulators, indicating lncRNA-chromatin interaction. Knockdown of lncRNA RP11-390F4.3 abolishes METTL4-mediated tumor metastasis. We demonstrate that ZMIZ1 is an essential co-activator of HIF-1α. Conclusions We show that hypoxia results in enriched 6mA levels in mammalian tumor cells through METTL4. This METTL4-mediated nuclear 6mA deposition induces tumor metastasis through activating multiple metastasis-inducing genes. METTL4 is characterized as a potential therapeutic target in hypoxic tumors.
Data analysis guidelines for single-cell RNA-seq in biomedical studies and clinical applications
Authors: Min Su, Tao Pan, Qiu-Zhen Chen, Wei-Wei Zhou, Yi Gong, Gang Xu, Huan-Yu Yan, Si Li, Qiao-Zhen Shi, Ya Zhang, Xiao He, Chun-Jie Jiang, Shi-Cai Fan, Xia Li, Murray J. Cairns, Xi Wang, Yong-Sheng Li
Journal: Military Medical Research (2022)

The application of single-cell RNA sequencing (scRNA-seq) in biomedical research has advanced our understanding of the pathogenesis of disease and provided valuable insights into new diagnostic and therapeutic strategies. With the expansion of capacity for high-throughput scRNA-seq, including clinical samples, the analysis of these huge volumes of data has become a daunting prospect for researchers entering this field. Here, we review the workflow for typical scRNA-seq data analysis, covering raw data processing and quality control, basic data analysis applicable for almost all scRNA-seq data sets, and advanced data analysis that should be tailored to specific scientific questions. While summarizing the current methods for each analysis step, we also provide an online repository of software and wrapped-up scripts to support the implementation. Recommendations and caveats are pointed out for some specific analysis tasks and approaches. We hope this resource will be helpful to researchers engaging with scRNA-seq, in particular for emerging clinical applications.
Mpox (formerly monkeypox) in women: epidemiological features and clinical characteristics of mpox cases in Spain, April to November 2022
Authors: Alberto Vallejo-Plaza, Francisco Rodríguez-Cabrera, Victoria Hernando Sebastián, Bernardo R Guzmán Herrador, Patricia Santágueda Balader, Lucía García San Miguel Rodríguez-Alarcón, Asunción Díaz Franco, Ana Garzón Sánchez, María José Sierra Moros, Fernando Simón Soria, Berta Suárez Rodríguez
Journal: Eurosurveillance (2022)

Over 79,000 confirmed cases of mpox were notified worldwide between May and November 2022, most of them in men who have sex with men. Cases in women, for whom mpox might pose different risks, are rare, and Spain has reported more than one third of those in Europe. Using surveillance data, our study found similar time trends, but differences in delay of diagnosis, sexual transmission and signs and symptoms between men and women.
Results of an interventional HIV testing programme in the context of a mpox (formerly monkeypox) vaccination campaign in Latium Region, Italy, August to October 2022
Authors: Silvia Pittalis, Valentina Mazzotta, Nicoletta Orchi, Isabella Abbate, Roberta Gagliardini, Elisabetta Gennaro, Augusto Faticoni, Pierluca Piselli, Gabriella Rozera, Stefania Cicalini, Fabrizio Maggi, Enrico Girardi, Francesco Vaia, Andrea Antinori, Vincenzo Puro
Journal: Eurosurveillance (2022)

HIV testing was offered to 2,185 people receiving mpox (formerly monkeypox) vaccination, who reported not being HIV positive. Among them 390 were current PrEP users, and 131 had taken PrEP in the past. Of 958 individuals consenting testing, six were newly diagnosed with HIV. Two patients had symptomatic primary HIV infection. None of the six patients had ever taken PrEP. Mpox vaccination represents an important opportunity for HIV testing and counselling about risk reduction and PrEP.